Related papers: Dynamics and energetics of a molecular zipper unde…
Single-molecule experiments with optical tweezers have become an important tool to study the properties and mechanisms of biological systems, such as cells and nucleic acids. In particular, force unzipping experiments have been used to…
The probability distribution of the velocity of gas molecules in a closed container is described by the kinetic theory of gases. When molecules collide or impact the walls of a container, they exchange energy and momentum in accordance with…
We study the few-body physics of trapped atoms or molecules with electric or magnetic dipole moments aligned by an external field. Using exact numerical diagonalization appropriate for the strongly correlated regime, as well as a classical…
The dynamics of folding of proteins is studied by means of a phenomenological master equation. The energy distribution is taken as a truncated exponential for the misfolded states plus a native state sitting below the continuum. The…
We discuss the low-temperature dynamics of an elastic manifold driven through a random medium. For driving forces well below the $T=0$ depinning force, the medium advances via thermally activated hops over the energy barriers separating…
Molecular motors drive mechanical motions utilizing the free energy liberated from chemical reactions such as ATP hydrolysis. Although it is essential to know the efficiency of this free energy transduction, it has been a challenge due to…
We investigate a microscopic motor based on an externally controlled two-level system. One cycle of the motor operation consists of two strokes. Within each stroke, the two-level system is in contact with a given thermal bath and its energy…
We study a two-dimensional model for interacting colloidal particles which displays spontaneous clustering. Within this model we investigate the competition between the pinning to a periodic corrugation potential, and a sideways constant…
We calculate the Equation of State of a quark system interacting through a phenomenological potential: the Richardson's potential, at finite baryon density and zero temperature. In particular we study three different cases with different…
Single molecule manipulation techniques reveal that the mechanical resistance of a protein depends on the direction of the applied force. Using a lattice model of polymers, we show that changing the pulling direction leads to different…
Molecular dynamics simulations of folding in an off-lattice protein model reveal a nucleation scenario, in which a few well-defined contacts are formed with high probability in the transition state ensemble of conformations. Their…
Motivated by various recent experimental findings, we propose a dynamical model of intermittently self-propelled particles: active particles that recurrently switch between two modes of motion, namely an active run-state and a turn state,…
We study the finite-temperature dynamics of thin elastic sheets in a single-clamped cantilever configuration. This system is known to exhibit a tilt transition at which the preferred mean plane of the sheet shifts from horizontal to a plane…
Allosteric regulation is often viewed as thermodynamic in nature. However protein internal motions during an enzymatic reaction cycle can be slow hopping processes over numerous potential barriers. We propose that regulating molecules may…
The properties of a strongly interacting quark plasma are investigated by molecular dynamics method including non-abelian quark-quark potential. Our main goal is to study the thermalization process in this system. We find an interesting…
We introduce and analyse a mathematical model describing the dynamics of particles generated by charge-exchange interactions. The model extends the well-established exchange-driven growth model, previously studied in several works, by…
We introduce a discrete time microscopic single particle model for kinetic transport. The kinetics is modeled by a two-state Markov chain, the transport by deterministic advection plus a random space step. The position of the particle after…
The time-dependent work probability distribution function $P(W)$ is investigated analytically for a diffusing particle trapped by an anisotropic harmonic potential and driven by a nonconservative drift force in two dimensions. We find that…
Active suspensions composed of self-propelled colloidal particles are considered. Their propulsion of is generated by chemical reactions occurring by heterogeneous catalysis and diffusiophoresis coupling the concentration gradients of…
In driven nonlinear systems, phase locking is an intriguing effect leading to robust stationary states that are stable over extended ranges of control parameters. Recent experiments allow for exploring microscopic mechanisms underlying such…